Environmental Surveillance of Coronavirus in Malawi

With early and prolonged gastrointestinal shedding of SARS-CoV-2 during and after infection
regardless of presentation of symptoms, environmental surveillance provides a promising
monitoring tool for estimating circulating COVID-19 in a community, in the absence of clinical
testing. However, current methods of concentrating virus from wastewater (ultrafiltration, PEG
precipitation, and electronegative membrane adsorption) can readily co-purify contaminants that,
both hinder detection of virus RNA by PCR and, and also do not allow for subsequent processing of
virus in culture to determine viral viability and thus infectiousness. An attractive solution is to
construct high affinity binding reagents which specifically enrich for intact virus from large volumes
of wastewater. We propose the use of the SARS-CoV-2 entry receptor ACE-2 fused to tags (histidine
and streptavidin) for the purification of intact PCR detectable SARS-CoV-2 from wastewater using
magnetic beads.
A recent clinical surveillance study in Malawi illustrated a high prevalence (13.3%) of SARS-CoV2
present within the population (unpublished). However, currently only having 19 COVID-19 testing
sites, Malawi thus has limited capacity to facilitate large scale clinical surveillance. Within the
Malawi-Liverpool Welcome Trust previously established environmental surveillance systems in
place for typhoid have been utilized to monitor COVID-19 in wastewater from as early as May 2020.
Preliminary data shows that SARS-CoV-2 was detected in 19% of samples using the CDC N1 assay.
This limited dataset highlights the potential for large scale environmental surveillance of SARS-CoV-
2 to understand transmission hotspots and monitor intervention strategies in Malawi. This project will establish if tagged ACE-2 can be used to purify intact virus from wastewater and scaled up for
appropriate use in LMIC's, followed by establishing infectivity of purified virus and genomic analysis
following NGS.